public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int[] colIndx = param.GetMultiChoiceParam("x").Value;
int[] colIndy = param.GetMultiChoiceParam("y").Value;
if (colIndx.Length == 0){
processInfo.ErrString = "Please select some columns";
return;
}
if (colIndx.Length != colIndy.Length){
processInfo.ErrString = "Please select the same number of columns in the boxes for the first and second columns.";
return;
}
int typeInd = param.GetSingleChoiceParam("Distribution type").Value;
int points = param.GetIntParam("Number of points").Value;
for (int k = 0; k < colIndx.Length; k++){
float[] xvals = GetColumn(mdata, colIndx[k]);
float[] yvals = GetColumn(mdata, colIndy[k]);
float[] xvals1;
float[] yvals1;
NumUtils.GetValidPairs(xvals, yvals, out xvals1, out yvals1);
double xmin;
double xmax;
double ymin;
double ymax;
DensityEstimation.CalcRanges(xvals1, yvals1, out xmin, out xmax, out ymin, out ymax);
float[,] values = DensityEstimation.GetValuesOnGrid(xvals1, xmin, (xmax - xmin)/points, points, yvals1, ymin,
(ymax - ymin)/points, points);
if (typeInd == 1 || typeInd == 3){
MakeConditional1(values);
}
if (typeInd == 2 || typeInd == 3){
MakeConditional2(values);
}
DensityEstimation.DivideByMaximum(values);
double[] xmat = new double[points];
for (int i = 0; i < points; i++){
xmat[i] = xmin + i*(xmax - xmin)/points;
}
double[] ymat = new double[points];
for (int i = 0; i < points; i++){
ymat[i] = ymin + i*(ymax - ymin)/points;
}
float[,] percvalues = CalcExcludedPercentage(values);
double[] dvals = new double[xvals.Length];
double[] pvals = new double[xvals.Length];
for (int i = 0; i < dvals.Length; i++){
double xx = xvals[i];
double yy = yvals[i];
if (!double.IsNaN(xx) && !double.IsNaN(yy)){
int xind = ArrayUtils.ClosestIndex(xmat, xx);
int yind = ArrayUtils.ClosestIndex(ymat, yy);
dvals[i] = values[xind, yind];
pvals[i] = percvalues[xind, yind];
} else{
dvals[i] = double.NaN;
pvals[i] = double.NaN;
}
}
string xname = GetColumnName(mdata, colIndx[k]);
string yname = GetColumnName(mdata, colIndy[k]);
mdata.AddNumericColumn("Density_" + xname + "_" + yname,
"Density of data points in the plane spanned by the columns " + xname + " and " + yname + ".", dvals);
mdata.AddNumericColumn("Excluded fraction_" + xname + "_" + yname,
"Percentage of points with a point density smaller than at this point in the plane spanned by the columns " + xname +
" and " + yname + ".", pvals);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ProcessInfo processInfo)
{
int numQuantiles = param.GetIntParam("Number of quantiles").Value;
int[] colInds = param.GetMultiChoiceParam("Columns").Value;
foreach (int colInd in colInds){
float[] vals = mdata.GetExpressionColumn(colInd);
List<int> v = new List<int>();
for (int i = 0; i < vals.Length; i++){
if (!float.IsNaN(vals[i])){
v.Add(i);
}
}
int[] o = v.ToArray();
vals = ArrayUtils.SubArray(vals, o);
int[] q = ArrayUtils.Order(vals);
o = ArrayUtils.SubArray(o, q);
string[][] catCol = new string[mdata.RowCount][];
for (int i = 0; i < catCol.Length; i++){
catCol[i] = new[]{"missing"};
}
for (int i = 0; i < o.Length; i++){
int catVal = (i*numQuantiles)/o.Length + 1;
catCol[o[i]] = new[]{"Q" + catVal};
}
string name = mdata.ExpressionColumnNames[colInd] + "_q";
string desc = "The column " + mdata.ExpressionColumnNames[colInd] + " has been divided into " + numQuantiles +
" quantiles.";
mdata.AddCategoryColumn(name, desc, catCol);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
const bool rows = false;
int minValids = param.GetIntParam("Min. number of values").Value;
SingleChoiceWithSubParams modeParam = param.GetSingleChoiceWithSubParams("Mode");
int modeInd = modeParam.Value;
if (modeInd != 0 && mdata.CategoryRowNames.Count == 0){
processInfo.ErrString = "No grouping is defined.";
return;
}
if (modeInd != 0){
processInfo.ErrString = "Group-wise filtering can only be appled to rows.";
return;
}
SingleChoiceWithSubParams x = param.GetSingleChoiceWithSubParams("Values should be");
Parameters subParams = x.GetSubParameters();
int shouldBeIndex = x.Value;
FilteringMode filterMode;
double threshold = double.NaN;
double threshold2 = double.NaN;
switch (shouldBeIndex){
case 0:
filterMode = FilteringMode.Valid;
break;
case 1:
filterMode = FilteringMode.GreaterThan;
threshold = subParams.GetDoubleParam("Minimum").Value;
break;
case 2:
filterMode = FilteringMode.GreaterEqualThan;
threshold = subParams.GetDoubleParam("Minimum").Value;
break;
case 3:
filterMode = FilteringMode.LessThan;
threshold = subParams.GetDoubleParam("Maximum").Value;
break;
case 4:
filterMode = FilteringMode.LessEqualThan;
threshold = subParams.GetDoubleParam("Maximum").Value;
break;
case 5:
filterMode = FilteringMode.Between;
threshold = subParams.GetDoubleParam("Minimum").Value;
threshold2 = subParams.GetDoubleParam("Maximum").Value;
break;
case 6:
filterMode = FilteringMode.Outside;
threshold = subParams.GetDoubleParam("Minimum").Value;
threshold2 = subParams.GetDoubleParam("Maximum").Value;
break;
default:
throw new Exception("Should not happen.");
}
if (modeInd != 0){
int gind = modeParam.GetSubParameters().GetSingleChoiceParam("Grouping").Value;
string[][] groupCol = mdata.GetCategoryRowAt(gind);
NonzeroFilterGroup(minValids, mdata, param, modeInd == 2, threshold, threshold2, filterMode, groupCol);
} else{
NonzeroFilter1(rows, minValids, mdata, param, threshold, threshold2, filterMode);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ProcessInfo processInfo)
{
bool rows = param.GetSingleChoiceParam("Matrix access").Value == 0;
bool atLeast = param.GetSingleChoiceParam("Side").Value == 0;
int numValids = param.GetIntParam("Number of valid values").Value;
SingleChoiceWithSubParams modeParam = param.GetSingleChoiceWithSubParams("Mode");
int modeInd = modeParam.Value;
if (modeInd != 0 && mdata.CategoryRowNames.Count == 0){
processInfo.ErrString = "No grouping is defined.";
return;
}
if (modeInd != 0 && !rows){
processInfo.ErrString = "Group-wise filtering can only be appled to rows.";
return;
}
if (modeInd != 0){
int gind = modeParam.GetSubParameters().GetSingleChoiceParam("Grouping").Value;
string[][] groupCol = mdata.CategoryRows[gind];
ValidValueFilterGroup(numValids, mdata, param, modeInd == 2, groupCol, atLeast);
} else{
ValidValueFilter1(rows, numValids, mdata, param, atLeast);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int minCount = param.GetIntParam("Min. count").Value;
int selCol = param.GetSingleChoiceParam("Selection").Value;
string value = param.GetStringParam("Value").Value;
int[] catIndices = param.GetMultiChoiceParam("Categories").Value;
bool[] selection = null;
if (selCol < mdata.CategoryColumnCount){
selection = new bool[mdata.RowCount];
string[][] x = mdata.GetCategoryColumnAt(selCol);
for (int i = 0; i < selection.Length; i++){
if (x[i] != null){
for (int j = 0; j < x[i].Length; j++){
if (x[i][j].Equals(value)){
selection[i] = true;
break;
}
}
}
}
}
CountingResult result = CountCategories(mdata, selection, selCol, catIndices);
CreateMatrixData(result, mdata, minCount, selection);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int avType = param.GetSingleChoiceParam("Average type").Value;
if (mdata.CategoryRowCount == 0){
processInfo.ErrString = "No category rows were loaded.";
return;
}
int groupColInd = param.GetSingleChoiceParam("Grouping").Value;
int validVals = param.GetIntParam("Min. valid values per group").Value;
bool keep = param.GetBoolParam("Keep original data").Value;
bool sdev = param.GetBoolParam("Add standard deviation").Value;
Func<IList<double>, double> func;
switch (avType){
case 0:
func = ArrayUtils.Median;
break;
case 1:
func = ArrayUtils.Mean;
break;
case 2:
func = ArrayUtils.Sum;
break;
case 3:
func = ArrayUtils.GeometricMean;
break;
default:
throw new Exception("Never get here.");
}
if (sdev) {
AddStandardDeviation(groupColInd, validVals, mdata);
}
if (keep) {
FillMatrixKeep(groupColInd, validVals, mdata, func);
} else{
FillMatrixDontKeep(groupColInd, validVals, mdata, func);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int nrows = param.GetIntParam("Number of rows").Value;
nrows = Math.Min(nrows, mdata.RowCount);
Random2 rand = new Random2();
int[] rows = ArrayUtils.SubArray(rand.NextPermutation(mdata.RowCount), nrows);
PerseusPluginUtils.FilterRows(mdata, param, rows);
}